Than you for the great theme. I understand its easy to change the colors, by hand, but it would be much easier to tweak the color combination with some sort of a color picker or something while customizing the website.
You could put those colors in a php file and override the css with !important at rendertime. These colors to be changed via two colorpickers that, in theory, can update the website in real-time. Like having most site pieces in the editing page and while color picking, update the css dynamically.
Another suggestion would be creating 2 styles with background or fill or whatever with the 2 colors and add them in the divs / class wherever it is used. Then some sort of an involvement of colorpickers for the same result.
Not that intimate with css but perhaps this could provide a fast, cheap and easy idea for this very asked-for feature.
Personally I find the tediousness of tweaking the colors the re-re-re-request for this feature.
We can only ask, and hope, and beg ??
Cheers!